4KS7

PAK6 kinase domain in complex with PF-3758309


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2C30PDB entry 2C30

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP827730% (v/v) isopropanol, 0.1M Bicine, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties
Matthews coefficientSolvent content
2.1943.81

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 48.573α = 90
b = 59.709β = 90
c = 100.541γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315mirrors2012-06-18MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 24-ID-E0.97922APS24-ID-E

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Sym I (Observed)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
11.4501000.07119.97757856
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.41.451000.8251.576.1

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB entry 2C301.437.7154855293099.680.19460.193350.21748RANDOM21.972
Temperature Factor Modeling
Anisotropic B[1][1]Anisotropic B[1][2]Anisotropic B[1][3]Anisotropic B[2][2]Anisotropic B[2][3]Anisotropic B[3][3]
-0.10.95-0.85
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.865
r_dihedral_angle_4_deg15.233
r_dihedral_angle_3_deg12.658
r_dihedral_angle_1_deg5.999
r_scbond_it2.43
r_mcangle_it2.269
r_angle_refined_deg2.034
r_mcbond_it1.6
r_chiral_restr0.119
r_bond_refined_d0.016
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.865
r_dihedral_angle_4_deg15.233
r_dihedral_angle_3_deg12.658
r_dihedral_angle_1_deg5.999
r_scbond_it2.43
r_mcangle_it2.269
r_angle_refined_deg2.034
r_mcbond_it1.6
r_chiral_restr0.119
r_bond_refined_d0.016
r_gen_planes_refined0.011
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2295
Nucleic Acid Atoms
Solvent Atoms258
Heterogen Atoms39

Software

Software
Software NamePurpose
PHASERphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling